System.currentTimeMillis vs System.nanoTime
If you're just looking for extremely precise measurements of elapsed time, use System.nanoTime(). System.currentTimeMillis() will give you the most accurate possible elapsed time in milliseconds since the epoch, but System.nanoTime() gives you a nanosecond-precise time, relative to some arbitrary point.
From the Java Documentation:
public static long nanoTime()Returns the current value of the most precise available system timer, in nanoseconds.
This method can only be used to measure elapsed time and is not related to any other notion of system or wall-clock time. The value returned represents nanoseconds since some fixed but arbitrary origin time (perhaps in the future, so values may be negative). This method provides nanosecond precision, but not necessarily nanosecond accuracy. No guarantees are made about how frequently values change. Differences in successive calls that span greater than approximately 292 years (263 nanoseconds) will not accurately compute elapsed time due to numerical overflow.
For example, to measure how long some code takes to execute:
long startTime = System.nanoTime();
// ... the code being measured ...
long estimatedTime = System.nanoTime() - startTime;
See also: JavaDoc System.nanoTime() and JavaDoc System.currentTimeMillis() for more info.
Since no one else has mentioned this…
It is not safe to compare the results of System.nanoTime() calls between different threads. Even if the events of the threads happen in a predictable order, the difference in nanoseconds can be positive or negative.
System.currentTimeMillis() is safe for use between threads.
Update by Arkadiy: I've observed more correct behavior of System.currentTimeMillis() on Windows 7 in Oracle Java 8. The time was returned with 1 millisecond precision. The source code in OpenJDK has not changed, so I do not know what causes the better behavior.
David Holmes of Sun posted a blog article a couple years ago that has a very detailed look at the Java timing APIs (in particular System.currentTimeMillis() and System.nanoTime()), when you would want to use which, and how they work internally.
Inside the Hotspot VM: Clocks, Timers and Scheduling Events - Part I - Windows
One very interesting aspect of the timer used by Java on Windows for APIs that have a timed wait parameter is that the resolution of the timer can change depending on what other API calls may have been made - system wide (not just in the particular process). He shows an example where using Thread.sleep() will cause this resolution change.